Research workbench
Saccharomyces cerevisiae phosphoglycerate mutase in complex with benzene hexacarboxylate
Analyse Saccharomyces cerevisiae phosphoglycerate mutase in complex with benzene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BQ4
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (phosphoglycerate mutase 1)
- EC
- 5.4.2.1
- UniProt
- P00950
- Ligands
- BHC, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Protein (phosphoglycerate mutase 1) (EC 5.4.2.1) | protein | 234 | 41% helix, 14% strand | P00950 |
| C, B | Protein (phosphoglycerate mutase 1) (EC 5.4.2.1) | protein | 235 | 40% helix, 14% strand | P00950 |
Ligands and binding sites
- BHC · Benzene hexacarboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.75 | 0.84 | 57 | empty |
| 2 | 370 | 0.73 | 0.84 | 50 | empty |
| 3 | 164 | 0.60 | 0.83 | 25 | SO4 |
| 4 | 173 | 0.59 | 0.82 | 23 | BHC |
| 5 | 202 | 0.58 | 0.81 | 27 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1004 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 969 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 924 Ų buried · 15 hydrogen bonds · protein-protein
- D–B · 919 Ų buried · 14 hydrogen bonds · protein-protein
- C–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1BQ4 · Saccharomyces cerevisiae phosphoglycerate mutase in complex with benzene hexacarboxylate · the same entry in another collection · chain D against D, TM-score 1.00
- P00950 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P00950) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00950
- Elsewhere: RCSB PDB 1BQ4 · PDBe 1BQ4 · UniProt P00950
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